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Structure paper

TitleStructural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient.
Journal, issue, pagesNat Struct Mol Biol, Vol. 27, Issue 10, Page 950-958, Year 2020
Publish dateJul 31, 2020
AuthorsDaming Zhou / Helen M E Duyvesteyn / Cheng-Pin Chen / Chung-Guei Huang / Ting-Hua Chen / Shin-Ru Shih / Yi-Chun Lin / Chien-Yu Cheng / Shu-Hsing Cheng / Yhu-Chering Huang / Tzou-Yien Lin / Che Ma / Jiandong Huo / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila Rijal / Robert F Donat / Kerry Godwin / Karen R Buttigieg / Julia A Tree / Julika Radecke / Neil G Paterson / Piyada Supasa / Juthathip Mongkolsapaya / Gavin R Screaton / Miles W Carroll / Javier Gilbert-Jaramillo / Michael L Knight / William James / Raymond J Owens / James H Naismith / Alain R Townsend / Elizabeth E Fry / Yuguang Zhao / Jingshan Ren / David I Stuart / Kuan-Ying A Huang /
PubMed AbstractThe COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID- ...The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds the receptor binding domain (RBD) of the viral spike glycoprotein tightly (K of 2 nM), and a 2.6-Å-resolution crystal structure of an RBD-EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues within this footprint are key to stabilizing the pre-fusion spike. Cryo-EM analyses of the pre-fusion spike incubated with EY6A Fab reveal a complex of the intact spike trimer with three Fabs bound and two further multimeric forms comprising the destabilized spike attached to Fab. EY6A binds what is probably a major neutralizing epitope, making it a candidate therapeutic for COVID-19.
External linksNat Struct Mol Biol / PubMed:32737466
MethodsEM (single particle) / X-ray diffraction
Resolution2.65 - 4.7 Å
Structure data

11173

6zdg

EMDB-11173, PDB-6zdg:
Association of three complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab
Method: EM (single particle) / Resolution: 4.7 Å

11174

6zdh

EMDB-11174, PDB-6zdh:
SARS-CoV-2 Spike glycoprotein in complex with a neutralizing antibody EY6A Fab
Method: EM (single particle) / Resolution: 3.7 Å

11184

6zfo

EMDB-11184, PDB-6zfo:
Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab
Method: EM (single particle) / Resolution: 4.4 Å

PDB-6zcz:
Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary complex with EY6A Fab and a nanobody.
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-6zer:
Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with EY6A Fab
Method: X-RAY DIFFRACTION / Resolution: 3.8 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-CL:
Unknown entry / Chloride

ChemComp-MG:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION / Phosphate

Source
  • severe acute respiratory syndrome coronavirus 2
  • human (human)
  • homo sapiens (human)
  • lama glama (llama)
KeywordsVIRAL PROTEIN / EY6a / RBD / Spike glycoprotein / SARS-CoV-2 / human neutralizing antibody / IMMUNE SYSTEM / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex

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